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In all of the discussions about driving down the cost of sequencing, I haven't seen much about the cost of nucleotides (or fluorescent nucleotides, for that matter). Genomic target enrichment methods (e.g., Nimblegen arrays) rely on (expensive) synthetic DNA on, or cleaved off of, microarray surfaces. Costs of standard oligos such as universal primers can be amortized over many samples, but as we approach the $1000 or even the $100 genome, costs of nucleotides and enzymes for PCR or phosphoramidites for custom oligo synthesis may become a factor. Is anyone aware of technology that could drive down these costs? Maybe the single molecule sequencing methods like Helicos or DNA nanopores will have a better chance once all of the reagent costs are factored in.
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This falls in line with my own reflections. None of the currently sold new-generation sequencing methods can cope with a sample containing the entire human genome in single run. And there is no need for that because most disease phenotypes correlate with mutations found within exons or in their vicinity, and these account for 1 to 2% human genome or about 60Mb of the total sequence. This is why the enrichment question is in the focus of the current research.
There is an explosive growth in the number of papers addressing the enrichment for exons. I have not read all of them, but those I have invariably use “programmable microarrays” containing many thousands of unique primers. In my childhood I attempted just to count from 1 to 1000 and found it a hard job.
Does anybody know the approximate price of a programmable microarray containing, say, 385,000 tiled oligonucleotides corresponding to 30,000 exons (Hodges et al., et al.,2007, Nat Genet Nov 4: [Epub ahead of print]). -
At some point recently I remember reading that Nimblegen was offering a giveaway of 15 custom arrays to the person/lab who proposed the best experiment. In the contest rules they stated the retail value of that prize to be $18,000US...which translates to ~$1200 per chip.Originally posted by Michael L. Altshuler View Post
Not too bad, and they undoubtedly have at least 50% margin in that cost. So if you're buying in bulk now I'm sure you can get the chip cost well below $1000.Comment
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The cost of a programable array with 385k feature is ~$500. that of 2.1M featuree is ~$1000.Comment
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Data variability is still an issue in sequencing technologies despite the advances in reproducibility and accuracy of these platforms. But the problem does not originate in the sequencing itself, but in the previous steps, before the sample reaches the sequencer.
The first step is collection, followed by preservation and sample preparation for analysis. Most scientists overlook those steps, but not being careful might just be skewing the experiment’s results.
...06-02-2026, 10:05 AM -
With the launch of new single-cell sequencing platforms in 2026, the field stands at an exciting inflection point. This article surveys the most impactful advances in the field and discusses how they’re reshaping research in cancer, immunology, and beyond.
Introduction
Single-cell sequencing technologies have undergone remarkable advances over the past decade, transitioning from low-throughput experimental approaches to highly scalable platforms capable of...05-22-2026, 06:42 AM
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